de.jstacs.data.sequences
Class RecursiveSequence

java.lang.Object
  extended by de.jstacs.data.Sequence
      extended by de.jstacs.data.sequences.RecursiveSequence
All Implemented Interfaces:
Comparable<Sequence>
Direct Known Subclasses:
PermutedSequence, Sequence.CompositeSequence, Sequence.SubSequence

public abstract class RecursiveSequence
extends Sequence

This is the main class for subsequences, composite sequences, ... . All these sequences are defined on an existing Sequence. After creating an RecursiveSequence, no SequenceAnnotation of the internally Sequence is returned by Sequence.getAnnotation(), ...

Author:
Jens Keilwagen

Nested Class Summary
 
Nested classes/interfaces inherited from class de.jstacs.data.Sequence
Sequence.CompositeSequence, Sequence.SubSequence
 
Field Summary
protected  Sequence content
          The internal sequence.
 
Fields inherited from class de.jstacs.data.Sequence
alphabetCon, annotation, rc
 
Constructor Summary
RecursiveSequence(AlphabetContainer alphabet, Sequence seq)
          Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.
RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
          Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.
 
Method Summary
 double continuousVal(int pos)
          Returns the continuous value at position pos of the Sequence.CompositeSequence.
 int discreteVal(int pos)
          Returns the discrete value at position pos of the Sequence.CompositeSequence.
protected abstract  int getIndex(int pos)
          Returns the index in the internal sequence.
 
Methods inherited from class de.jstacs.data.Sequence
annotate, compareTo, complement, complement, create, create, create, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

content

protected Sequence content
The internal sequence.

Constructor Detail

RecursiveSequence

public RecursiveSequence(AlphabetContainer alphabet,
                         SequenceAnnotation[] annotation,
                         Sequence seq)
Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

Parameters:
alphabet - the AlphabetContainer
annotation - the annotation of the RecursiveSequence
seq - the sequence
See Also:
Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

RecursiveSequence

public RecursiveSequence(AlphabetContainer alphabet,
                         Sequence seq)
Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

Parameters:
alphabet - the AlphabetContainer
seq - the sequence
Method Detail

continuousVal

public double continuousVal(int pos)
Description copied from class: Sequence
Returns the continuous value at position pos of the Sequence.CompositeSequence.

Specified by:
continuousVal in class Sequence
Parameters:
pos - the position of the Sequence.CompositeSequence
Returns:
the continuous value at position pos of the Sequence.CompositeSequence

discreteVal

public int discreteVal(int pos)
Description copied from class: Sequence
Returns the discrete value at position pos of the Sequence.CompositeSequence.

Specified by:
discreteVal in class Sequence
Parameters:
pos - the position of the Sequence.CompositeSequence
Returns:
the discrete value at position pos of the Sequence.CompositeSequence

getIndex

protected abstract int getIndex(int pos)
Returns the index in the internal sequence.

Parameters:
pos - the index in the external sequence
Returns:
the index in the internal sequence